Starting phenix.real_space_refine on Mon Jun 24 16:06:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znd_60268/06_2024/8znd_60268_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znd_60268/06_2024/8znd_60268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znd_60268/06_2024/8znd_60268.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znd_60268/06_2024/8znd_60268.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znd_60268/06_2024/8znd_60268_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znd_60268/06_2024/8znd_60268_updated.pdb" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 14 5.16 5 C 2104 2.51 5 N 563 2.21 5 O 650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 5": "OD1" <-> "OD2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A ASP 209": "OD1" <-> "OD2" Residue "A ASP 244": "OD1" <-> "OD2" Residue "A ASP 256": "OD1" <-> "OD2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 390": "OD1" <-> "OD2" Residue "A ARG 396": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 3334 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3262 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 72 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1, 'water': 24} Link IDs: {None: 24} Time building chain proxies: 2.86, per 1000 atoms: 0.86 Number of scatterers: 3334 At special positions: 0 Unit cell: (66.176, 63.92, 70.688, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 3 15.00 O 650 8.00 N 563 7.00 C 2104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 664.2 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 758 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 4 sheets defined 48.3% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 6 through 20 removed outlier: 3.765A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N TYR A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 80 through 96 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 117 through 134 removed outlier: 6.009A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 190 through 206 Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.728A pdb=" N TYR A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 281 through 285 removed outlier: 3.556A pdb=" N LEU A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 285' Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 324 through 333 removed outlier: 4.023A pdb=" N ASP A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 343 No H-bonds generated for 'chain 'A' and resid 340 through 343' Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 366 through 391 Processing helix chain 'A' and resid 395 through 414 Processing sheet with id= A, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.643A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY A 104 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 72 through 75 removed outlier: 6.866A pdb=" N GLY A 106 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N HIS A 75 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE A 108 " --> pdb=" O HIS A 75 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 291 through 294 removed outlier: 6.312A pdb=" N THR A 238 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N VAL A 217 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N VAL A 240 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 242 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 313 through 315 removed outlier: 7.016A pdb=" N LEU A 336 " --> pdb=" O VAL A 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 153 hydrogen bonds defined for protein. 447 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.96 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1069 1.34 - 1.46: 465 1.46 - 1.57: 1820 1.57 - 1.69: 5 1.69 - 1.81: 27 Bond restraints: 3386 Sorted by residual: bond pdb=" O2B NDP A 500 " pdb=" P2B NDP A 500 " ideal model delta sigma weight residual 1.833 1.607 0.226 3.80e-02 6.93e+02 3.53e+01 bond pdb=" O5D NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 1.757 1.596 0.161 3.50e-02 8.16e+02 2.13e+01 bond pdb=" N TYR A 250 " pdb=" CA TYR A 250 " ideal model delta sigma weight residual 1.455 1.413 0.042 1.25e-02 6.40e+03 1.15e+01 bond pdb=" C2B NDP A 500 " pdb=" O2B NDP A 500 " ideal model delta sigma weight residual 1.330 1.419 -0.089 2.90e-02 1.19e+03 9.52e+00 bond pdb=" CA TYR A 250 " pdb=" C TYR A 250 " ideal model delta sigma weight residual 1.520 1.487 0.034 1.22e-02 6.72e+03 7.60e+00 ... (remaining 3381 not shown) Histogram of bond angle deviations from ideal: 99.94 - 106.78: 123 106.78 - 113.61: 1848 113.61 - 120.44: 1293 120.44 - 127.28: 1288 127.28 - 134.11: 46 Bond angle restraints: 4598 Sorted by residual: angle pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 107.74 129.93 -22.19 1.95e+00 2.62e-01 1.29e+02 angle pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " ideal model delta sigma weight residual 103.84 119.43 -15.59 1.91e+00 2.73e-01 6.63e+01 angle pdb=" C5D NDP A 500 " pdb=" O5D NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 104.93 118.60 -13.67 2.66e+00 1.41e-01 2.64e+01 angle pdb=" O2N NDP A 500 " pdb=" PN NDP A 500 " pdb=" O5D NDP A 500 " ideal model delta sigma weight residual 100.52 109.34 -8.82 1.91e+00 2.74e-01 2.13e+01 angle pdb=" O1X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.46 112.28 5.18 1.17e+00 7.36e-01 1.97e+01 ... (remaining 4593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.43: 1872 23.43 - 46.87: 110 46.87 - 70.30: 17 70.30 - 93.73: 9 93.73 - 117.16: 1 Dihedral angle restraints: 2009 sinusoidal: 820 harmonic: 1189 Sorted by residual: dihedral pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " ideal model delta sinusoidal sigma weight residual 175.04 57.88 117.16 1 3.00e+01 1.11e-03 1.55e+01 dihedral pdb=" CA PHE A 341 " pdb=" C PHE A 341 " pdb=" N LEU A 342 " pdb=" CA LEU A 342 " ideal model delta harmonic sigma weight residual 180.00 162.32 17.68 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CB GLU A 288 " pdb=" CG GLU A 288 " pdb=" CD GLU A 288 " pdb=" OE1 GLU A 288 " ideal model delta sinusoidal sigma weight residual 0.00 -89.63 89.63 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 2006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 381 0.047 - 0.093: 79 0.093 - 0.140: 36 0.140 - 0.186: 2 0.186 - 0.233: 3 Chirality restraints: 501 Sorted by residual: chirality pdb=" C4D NDP A 500 " pdb=" C3D NDP A 500 " pdb=" C5D NDP A 500 " pdb=" O4D NDP A 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.48 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA TYR A 250 " pdb=" N TYR A 250 " pdb=" C TYR A 250 " pdb=" CB TYR A 250 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C1B NDP A 500 " pdb=" C2B NDP A 500 " pdb=" N9A NDP A 500 " pdb=" O4B NDP A 500 " both_signs ideal model delta sigma weight residual False 2.59 2.40 0.19 2.00e-01 2.50e+01 8.86e-01 ... (remaining 498 not shown) Planarity restraints: 586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4N NDP A 500 " 0.018 2.00e-02 2.50e+03 3.11e-02 9.68e+00 pdb=" C5N NDP A 500 " -0.039 2.00e-02 2.50e+03 pdb=" C6N NDP A 500 " 0.040 2.00e-02 2.50e+03 pdb=" N1N NDP A 500 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 500 " 0.031 2.00e-02 2.50e+03 1.92e-02 4.62e+00 pdb=" C3N NDP A 500 " 0.004 2.00e-02 2.50e+03 pdb=" C4N NDP A 500 " 0.005 2.00e-02 2.50e+03 pdb=" C7N NDP A 500 " -0.016 2.00e-02 2.50e+03 pdb=" N1N NDP A 500 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 141 " 0.031 5.00e-02 4.00e+02 4.62e-02 3.42e+00 pdb=" N PRO A 142 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.025 5.00e-02 4.00e+02 ... (remaining 583 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1224 2.89 - 3.39: 3352 3.39 - 3.90: 6107 3.90 - 4.40: 7003 4.40 - 4.90: 11343 Nonbonded interactions: 29029 Sorted by model distance: nonbonded pdb=" NE ARG A 73 " pdb=" OE1 GLU A 78 " model vdw 2.392 2.520 nonbonded pdb=" O VAL A 401 " pdb=" OG SER A 405 " model vdw 2.402 2.440 nonbonded pdb=" OD1 ASP A 5 " pdb=" OG SER A 81 " model vdw 2.440 2.440 nonbonded pdb=" N ASP A 145 " pdb=" OG1 THR A 148 " model vdw 2.495 2.520 nonbonded pdb=" NZ LYS A 177 " pdb=" OD1 ASN A 358 " model vdw 2.504 2.520 ... (remaining 29024 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.420 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.040 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.226 3386 Z= 0.434 Angle : 0.927 22.188 4598 Z= 0.525 Chirality : 0.048 0.233 501 Planarity : 0.005 0.047 586 Dihedral : 15.596 117.160 1251 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.88 % Allowed : 0.59 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.42), residues: 414 helix: 2.03 (0.35), residues: 202 sheet: -0.23 (0.63), residues: 72 loop : -0.97 (0.52), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.002 0.001 HIS A 61 PHE 0.015 0.002 PHE A 341 TYR 0.015 0.002 TYR A 363 ARG 0.004 0.000 ARG A 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 0.397 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 84 average time/residue: 1.5746 time to fit residues: 135.2306 Evaluate side-chains 59 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3386 Z= 0.173 Angle : 0.453 4.515 4598 Z= 0.240 Chirality : 0.042 0.122 501 Planarity : 0.005 0.046 586 Dihedral : 6.623 98.611 462 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.18 % Allowed : 10.62 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.42), residues: 414 helix: 2.06 (0.36), residues: 206 sheet: -0.02 (0.64), residues: 72 loop : -0.83 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 382 HIS 0.004 0.001 HIS A 388 PHE 0.015 0.001 PHE A 341 TYR 0.011 0.001 TYR A 363 ARG 0.007 0.001 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.394 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 70 average time/residue: 1.3882 time to fit residues: 99.7308 Evaluate side-chains 60 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.0370 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3386 Z= 0.163 Angle : 0.436 4.479 4598 Z= 0.230 Chirality : 0.041 0.123 501 Planarity : 0.005 0.047 586 Dihedral : 6.241 87.042 462 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.88 % Allowed : 13.27 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.42), residues: 414 helix: 2.14 (0.36), residues: 206 sheet: 0.24 (0.68), residues: 68 loop : -0.91 (0.52), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 PHE 0.013 0.001 PHE A 341 TYR 0.011 0.001 TYR A 363 ARG 0.007 0.001 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.419 Fit side-chains REVERT: A 246 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7234 (mpt180) REVERT: A 370 ARG cc_start: 0.7709 (ttm-80) cc_final: 0.7469 (ttm110) outliers start: 3 outliers final: 1 residues processed: 63 average time/residue: 1.5951 time to fit residues: 102.8738 Evaluate side-chains 60 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 246 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3386 Z= 0.123 Angle : 0.401 4.405 4598 Z= 0.210 Chirality : 0.040 0.124 501 Planarity : 0.004 0.047 586 Dihedral : 5.806 79.382 462 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.47 % Allowed : 13.57 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.42), residues: 414 helix: 2.29 (0.36), residues: 205 sheet: 0.45 (0.68), residues: 68 loop : -0.88 (0.51), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.001 0.000 HIS A 388 PHE 0.012 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.006 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.398 Fit side-chains REVERT: A 246 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7282 (mpt180) outliers start: 5 outliers final: 2 residues processed: 63 average time/residue: 1.4545 time to fit residues: 94.0601 Evaluate side-chains 63 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 277 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3386 Z= 0.246 Angle : 0.468 4.602 4598 Z= 0.248 Chirality : 0.043 0.127 501 Planarity : 0.005 0.049 586 Dihedral : 5.932 76.733 462 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.36 % Allowed : 13.57 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.42), residues: 414 helix: 2.12 (0.35), residues: 205 sheet: 0.41 (0.64), residues: 72 loop : -0.78 (0.52), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 382 HIS 0.002 0.001 HIS A 388 PHE 0.014 0.002 PHE A 341 TYR 0.014 0.001 TYR A 363 ARG 0.005 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.378 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 62 average time/residue: 1.7427 time to fit residues: 110.7515 Evaluate side-chains 62 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 304 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.0050 chunk 20 optimal weight: 0.0010 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 0.0870 chunk 22 optimal weight: 4.9990 overall best weight: 0.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3386 Z= 0.110 Angle : 0.395 4.377 4598 Z= 0.205 Chirality : 0.040 0.123 501 Planarity : 0.004 0.047 586 Dihedral : 5.232 65.711 462 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.59 % Allowed : 15.63 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.42), residues: 414 helix: 2.42 (0.35), residues: 204 sheet: 0.43 (0.73), residues: 63 loop : -0.67 (0.49), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.000 0.000 HIS A 267 PHE 0.010 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.009 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.421 Fit side-chains REVERT: A 333 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8555 (mtmm) outliers start: 2 outliers final: 0 residues processed: 65 average time/residue: 1.4303 time to fit residues: 95.3508 Evaluate side-chains 63 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.0030 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.0070 chunk 25 optimal weight: 4.9990 overall best weight: 0.5612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3386 Z= 0.116 Angle : 0.401 5.201 4598 Z= 0.206 Chirality : 0.040 0.123 501 Planarity : 0.004 0.046 586 Dihedral : 4.760 53.354 462 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.59 % Allowed : 17.11 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.42), residues: 414 helix: 2.49 (0.35), residues: 205 sheet: 0.45 (0.70), residues: 68 loop : -0.48 (0.51), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 382 HIS 0.001 0.000 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.008 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.464 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 66 average time/residue: 1.4688 time to fit residues: 99.5101 Evaluate side-chains 63 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3386 Z= 0.251 Angle : 0.478 5.024 4598 Z= 0.251 Chirality : 0.043 0.126 501 Planarity : 0.005 0.049 586 Dihedral : 5.015 50.242 462 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.18 % Allowed : 16.52 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.42), residues: 414 helix: 2.24 (0.35), residues: 205 sheet: 0.51 (0.65), residues: 72 loop : -0.70 (0.51), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 382 HIS 0.001 0.000 HIS A 267 PHE 0.014 0.002 PHE A 341 TYR 0.014 0.001 TYR A 363 ARG 0.008 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.380 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 59 average time/residue: 1.5080 time to fit residues: 91.2906 Evaluate side-chains 58 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.0980 chunk 33 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3386 Z= 0.250 Angle : 0.479 5.385 4598 Z= 0.253 Chirality : 0.044 0.127 501 Planarity : 0.005 0.050 586 Dihedral : 4.985 45.727 462 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.88 % Allowed : 16.52 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.41), residues: 414 helix: 2.13 (0.35), residues: 205 sheet: 0.46 (0.67), residues: 67 loop : -0.79 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.003 0.000 HIS A 267 PHE 0.013 0.002 PHE A 341 TYR 0.014 0.001 TYR A 363 ARG 0.005 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.398 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 60 average time/residue: 1.5669 time to fit residues: 96.2822 Evaluate side-chains 59 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 269 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.0000 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 9 optimal weight: 0.0570 chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 0.0170 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3386 Z= 0.115 Angle : 0.405 6.023 4598 Z= 0.209 Chirality : 0.040 0.122 501 Planarity : 0.004 0.048 586 Dihedral : 4.365 37.693 462 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.29 % Allowed : 17.11 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.42), residues: 414 helix: 2.40 (0.35), residues: 204 sheet: 0.56 (0.68), residues: 68 loop : -0.74 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 92 HIS 0.002 0.000 HIS A 267 PHE 0.008 0.001 PHE A 341 TYR 0.006 0.001 TYR A 363 ARG 0.007 0.000 ARG A 265 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.440 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 62 average time/residue: 1.3891 time to fit residues: 88.4363 Evaluate side-chains 61 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.113182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.088617 restraints weight = 4181.291| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.53 r_work: 0.2757 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3386 Z= 0.137 Angle : 0.419 6.553 4598 Z= 0.217 Chirality : 0.041 0.123 501 Planarity : 0.004 0.047 586 Dihedral : 4.360 38.910 462 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.29 % Allowed : 17.99 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.42), residues: 414 helix: 2.40 (0.35), residues: 205 sheet: 0.56 (0.69), residues: 68 loop : -0.70 (0.50), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.001 0.000 HIS A 388 PHE 0.011 0.001 PHE A 341 TYR 0.008 0.001 TYR A 225 ARG 0.006 0.000 ARG A 265 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2076.95 seconds wall clock time: 36 minutes 55.06 seconds (2215.06 seconds total)